Version-1997.0 Release Notes

Some of the changes in this release will not be obvious to the user. Many
changes were required to improve the Gap4 scripting language. We consider
this important as it puts us in a better position for future development
and allows other people to easily extend gap4 themselves. The first draft
of the documentation on this scripting system is now available and can be
dound in the scripting_manual/scripting_toc.html file.

The most noticable changes are within gap4, however two new programs have
also been added. Vector_clip is is a replacement for vepe, which is still
distributed at present. Trace_diff is a tool for comparing pairs of trace
files to produce a "difference" trace file and to automatically find and
mark mutations.

Gap4 has a much improved Template Display that can now display more than
one contig. This provides a much easier way of investigating the
relationships between contigs.

Gap4 editing has had several improvements too: it redisplays faster;
superedit now provides a larger diversity of editing abilities; a vertical
scrollbar, trace differencing, and showing disagreements by colour aid
using the editor for mutation studies; and the disassemble readings and
break contig functions now have interfaces available directly from within
the editor.

Trev has had a few updates to allow repositioning of the vector clips.
We've also fixed a couple of bugs to do with saving the accuracy values
after editing.

Pregap is now more robust and has an extra question to control whether it
should derive reading names from ABI samplenames (held within the files
themselves) or the ABI filenames.

Dynamic linking is now used for many programs. This should be transparent
to the user, but should use fewer system resources on crowded machines and
allows for greater flexibility. The programs using tcl and tk have been
updated to use tcl version 7.6 and tk version 4.2 to allow for on-the-fly
loading of dynamic libraries, which translate to "packages" to extend gap4,
sip4 or trev. See the scripting documentation for details.

Finally, trace file compression is better supported. Gap4 and trev can
compress and uncompress trace files (whatever format) on the fly, thus
allowing for significant reductions in disk space. The "gzip_trace" and
"bzip_trace" scripts can be used to compress your SCF files, saving around
70% of your disk space, which is equivalent to at least a 10 to 1
compression of ABI files.

A more verbose list of changes follows. Note though that only the more
important bug fixes are listed, and we consider those marked with asterisks
to be most important.

New Programs

The Template Display now supports displaying multiple contigs
including displaying their relative positions and overlapping data.
It also allows for their relative positions to be changed.

Major revamp of the gap4 scripting language including the first draft
of the scripting documentation.

Shuffle pads now removes places where there are columns of 100% pad.

The "align" button in the join editor now adjusts the relative offsets
between contigs when the alignment requires it. It used to insert
unnecessary pads instead.

Improved superedit to allow user control over which individual
editing functions are activated. Includes insertion to reads,
deletion to reads, insert of anything to consensus, deletion of
dash in consensus, deletion of anything in consensus, replacing of
bases in consensus, shifting readings, transposing any two
characters (usually only allows pads), and allowing uppercase for
changes/insertions. Each of these options can be independently
controlled.

Maximum database filename length is now 256. NB: this is not the
reading name length.

Vertical scrollbar in contig editor. Used when the height is greater
than a specified threshold.

Use of tcl7.6/tk4.2 (instead of 7.4/4.0). We utilise the tcl dynamic
loading strategy to allow arbitrary user defined extensions to be
added directly onto the main menus.

Improved handling of read only databases, including greying out of
menu items and a read-only editor mode.

Bug fix: Suggest Primers when only using one contig now works.

Bug fix: When assembling really long (4K) readings we now check that
adding pads doesn't overflow the maximum allowed length.

Directed assembly has improved memory usage checking. Better checking
of the tolerance used during assembly.

Automatic 'maxdb' parameter adjustment when opening large databases.
However it still needs to be hand set for large assembly runs.

Bug fix: Fixed rare crash in trace display.

Bug fix: Searching by tag type and annotation (in the editor) now
searches in order of the left end of the visible region. Previously we
searched on the left end, which caused some tags to be missed when
they overlapped between used and cutoff data.

Bug fix: Doctor database was reporting the 'referenced by' field of
annotations as one reading too high.

Melting temperature is now listed in the suggest probe output.

Bug fix: Doctor database's shift readings function works once again.

Added a "read pairs" only display mode of the template display to only
show templates containing both forward and reverse readings.

Added a Print List command in the list menu. Printing is also possible
from the main output window.

The editor "set output list" setting no longer clears the list. This
simplifies producing lists from several contigs.

Improved the list mechanism for auto-generated lists. A list named
"[contig_identifier]" will expand to all the readings within a contig.
A list named "{list_name}" will expand to all the readings within all
the contigs in a list (eg "{contigs}"). Additionally "allreadings" and
"allcontigs" lists are calculated on the fly.

Double left clicking on a match in the 2D plot now performs the
"obvious" operation (which is the one marked with an asterisk in
the popup menu).

Check assembly no longer brings up new editors when one exists, but
moves its displayed position instead.

Contig Editor speed and X network traffic usage has been improved,
specifically when editing single sequences or displaying very colour
rich screens.

Trace differencing added to the contig editor. We now have the ability
to compare any two traces to display differences, or to compare any
trace with a 'standard' comparator.

Bug fix: solved editor crashes where the quit button was pressed
either when busy (eg aligning) or just starting up.